And to come full circle, shortly after being supported by oligo, they will
be supported by frma.

Best,
Matt
 On Jan 14, 2014 11:19 AM, "Benilton Carvalho" <beniltoncarvalho@gmail.com>
wrote:

> I may have misunderstood what Steve described... So, I'm writing just to
> expose my version of what oligo does re: exon arrays:
>
> 1) oligo uses the official PGF/MPS files provided by Affymetrix to proceed
> with preprocessing;
>
> 2) given the design of the chip, there are different probeset definitions
> (which are given by Affymetrix through the MPS files). These different
> definitions are: core ("most reliable  evidence from RefSeq and full-length
> mRNA GenBank records"), extended ("supported by other cDNA evidence beyond
> what is used to support core probe sets") and full ("supported by
> computational gene prediction evidence only").
>
> 3) oligo uses the definitions above to perform preprocessing (this can be
> changed throught the 'target' argument in rma()). The user can also use the
> value 'probeset' to use the probeset definition given in the PGF.
>
> Now, re: what the BrainArray group does... they start with *only* chip
> coordinates and probe sequences, nothing else (note: this is independent
> from Affymetrix probeset definitions and, therefore, not related to the
> probeset definitions that we use in oligo - which come from Affymetrix).
> These sequences are then aligned and reannotated. This results in new
> probeset definitions, which they provide as what I call "BrainArray CDFs"
> (note that after this procedure, there is no such thing as
> core/full/extended probesets)....
>
> For the moment, oligo does not officially support the remapped CDFs. But
> that's something you should expect for the near future.
>
> b
>
>
> 2014/1/14 Ty Thomson <tthomson@selventa.com>
>
> > Hi Steve,
> >
> > Thanks, that makes a lot of sense.  I might just need to get another R
> > installation going so I can directly assess the effect of using all the
> > probes on my data.
> >
> > Regards,
> >
> > Ty
> >
> > -----Original Message-----
> > From: Steve Piccolo [mailto:stephen.piccolo@hsc.utah.edu]
> > Sent: Tuesday, January 14, 2014 9:35 AM
> > To: Ty Thomson; bioconductor@r-project.org
> > Subject: Re: using frma and brainarray cdf on exon arrays
> >
> > Hi Ty,
> >
> > The exon arrays have about 5 million probes. By default, the oligo
> package
> > uses only a subset of these probes, which have been flagged as being most
> > useful. However, the BrainArray package may want to include probes that
> are
> > not included by oligo. Thus it may be valuable to start with all probes
> > (exonarrayTarget=łprobeset˛) so that all probes included in the
> BrainArray
> > mappings will be included. The previous version of SCAN.UPC uses the
> > default oligo probes.
> >
> > Regards,
> > -Steve
> >
> > On 1/14/14, 7:27 AM, "Ty Thomson" <tthomson@selventa.com> wrote:
> >
> > >Hi Steve,
> > >
> > >Thanks for the suggestion.  I'm running bioconductor 2.12 with
> > >SCAN.UPC_2.0.2, and it doesn't look like this version of SCAN supports
> > >the exonArrayTarget parameter.  After reading the documentation for the
> > >exonArrayTarget parameter in the most recent version of SCAN I don't
> > >really understand exactly what it does.  Can you give me a bit more
> > >information on the difference when using a brain array CDF
> > >(probeSummaryPackage=hgu133plus2hsentrezgprobe) between what happens in
> > >my current version of SCAN and in the newest version when setting
> > >exonArrayTarget="probset"?  I am reluctant to change version of
> > >bioconductor mid-project for the effects this could have on other
> > >aspects of the project (and the potential need to re-run everything
> > again).
> > >
> > >Regards,
> > >
> > >Ty
> > >
> > >-----Original Message-----
> > >From: Steve Piccolo [mailto:stephen.piccolo@hsc.utah.edu]
> > >Sent: Tuesday, January 14, 2014 8:25 AM
> > >To: bioconductor@r-project.org; Ty Thomson
> > >Subject: Re: using frma and brainarray cdf on exon arrays
> > >
> > >Hi Ty,
> > >
> > >Another option is to try the SCAN.UPC package. It is also designed to
> > >support single-sample normalization. And it should be able to integrate
> > >the BrainArray annotations for the exon arrays. In the SCAN function,
> > >pay attention to the probeSummaryPackage and exonArrayTarget
> > >parameters. And the InstallBrainArrayPackage function may come in
> > >handy.  Let me know if you run into any troubles with it.
> > >
> > >Regards,
> > >-Steve
> > >
> > >
> > >
> > >On 1/14/14, 4:00 AM, "bioconductor-request@r-project.org"
> > ><bioconductor-request@r-project.org> wrote:
> > >
> > >>Date: Mon, 13 Jan 2014 20:25:44 +0000
> > >>From: Ty Thomson <tthomson@selventa.com>
> > >>To: Matthew McCall <mccallm@gmail.com>
> > >>Cc: "bioconductor@r-project.org" <bioconductor@r-project.org>
> > >>Subject: Re: [BioC] using frma and brainarray cdf on exon arrays
> > >>Message-ID:
> > >>
> > >><f71eeb981506499f9b6e0c317b4eb53a@CO2PR04MB601.namprd04.prod.outlook.c
> > >>o
> > >>m>
> > >>
> > >>Content-Type: text/plain; charset="iso-8859-1"
> > >>
> > >>Hi Matt,
> > >>
> > >>Thanks for the quick reply and the suggestions.  I'll look into making
> > >>my own pd annotation and frmavecs packages.
> > >>
> > >>Ty
> > >>
> > >>
> > >>-----Original Message-----
> > >>From: Matthew McCall [mailto:mccallm@gmail.com]
> > >>Sent: Monday, January 13, 2014 3:14 PM
> > >>To: Ty Thomson
> > >>Cc: bioconductor@r-project.org
> > >>Subject: Re: using frma and brainarray cdf on exon arrays
> > >>
> > >>Ty,
> > >>
> > >>Unfortunately, what you are attempting to do is not currently
> > >>implemented. The frmavecs packages for the 3' Affy arrays (HGU133a,
> > >>HGU133plus2, etc) contain implementations for both the Affy and
> > >>BrainArray CDFs. The issue is with the newer Affy arrays (HuGene 1.0
> > >>ST, etc.), which should really be read in using the oligo package and
> > >>corresponding pd annotation packages. This is implemented in frma for
> > >>the Affy annotation, but currently the BrainArray folks provide CDFs,
> > >>which can't be readily used. This may be changing fairly soon -- I
> > >>believe the BrainArray group may start offering oligo compatible
> > >>annotation packages.
> > >>Until then, to do what you would like would
> > >>require: (1) making your own pd annotation package corresponding to
> > >>the BrainArray alternative CDF, and (2) creating your own frmavecs
> > >>package for the alternative annotation.
> > >>
> > >>Best,
> > >>Matt
> > >>
> > >>
> > >>On Mon, Jan 13, 2014 at 2:53 PM, Ty Thomson <tthomson@selventa.com>
> > >>wrote:
> > >>>Apologies if any of my questions are na?ve, as I don't have a lot of
> > >>>experience with exon arrays.  I would like to analyze an Affy HuGene
> > >>>1.0 ST array using the brainArray CDF (because I want to get
> > >>>expression values on a per gene level), and use fRMA (to correct for
> > >>>batch effects and enable me to add additional samples in the future
> > >>>without redoing RMA).  Is this possible?  Here's what I've tried
> > >>>without much success thus far:
> > >>>
> > >>>
> > >>>
> > >>>I can skip brainarray and just load the data and run fRMA without
> error:
> > >>>
> > >>>>exonFS <- read.celfiles(filenames=cel.files, verbose=F,
> > >>>>celfile.path=NULL)
> > >>>
> > >>>>tmp.eset <- frma(exonFS, summarize="median_polish")
> > >>>
> > >>>
> > >>>
> > >>>But when I use ReadAffy and specify the cdf, fRMA generates an error:
> > >>>
> > >>>>Affybatch <- ReadAffy(filenames=cel.files, verbose=F,
> > >>>>celfile.path=NULL,
> > >>>>cdfname="hugene10sthsentrezg")
> > >>>
> > >>>Warning message:
> > >>>
> > >>>
> > >>>
> > >>>The affy package can process data from the Gene ST 1.x series of
> > >>>arrays,
> > >>>
> > >>>but you should consider using either the oligo or xps packages, which
> > >>>are specifically
> > >>>
> > >>>designed for these arrays.
> > >>>
> > >>>
> > >>>
> > >>>>tmp.eset <- frma(Affybatch, summarize="median_polish")
> > >>>
> > >>>Error in frmaMedPol(object, background, normalize, target,
> > >>>input.vecs,
> > >>>:
> > >>>
> > >>>   hugene10stfrmavecs package must be installed first
> > >>>
> > >>>In addition: Warning message:
> > >>>
> > >>>In library(package, lib.loc = lib.loc, character.only = TRUE,
> > >>>logical.return = TRUE,  :
> > >>>
> > >>>   there is no package called 'hugene10stfrmavecs'
> > >>>
> > >>>
> > >>>
> > >>>
> > >>>
> > >>>When I try running fRMA while directly passing the frmavecs to the
> > >>>function I get a different error:
> > >>>
> > >>>>data(hugene.1.0.st.v1frmavecs)
> > >>>
> > >>>>tmp.eset <- frma(Affybatch, summarize="median_polish",
> > >>>>input.vecs=hugene.1.0.st.v1frmavecs)
> > >>>
> > >>>Warning message:
> > >>>
> > >>>In log2(pms) - input.vecs$probeVec :
> > >>>
> > >>>   longer object length is not a multiple of shorter object length
> > >>>
> > >>>
> > >>>
> > >>>
> > >>>
> > >>>Thanks in advance for any help,
> > >>>
> > >>>
> > >>>
> > >>>Ty
> > >>>
> > >>>
> > >>>
> > >>>
> > >>>
> > >>>>sessionInfo()
> > >>>
> > >>>R version 3.0.1 (2013-05-16)
> > >>>
> > >>>Platform: x86_64-w64-mingw32/x64 (64-bit)
> > >>>
> > >>>
> > >>>
> > >>>locale:
> > >>>
> > >>>[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United
> > >>>States.1252    LC_MONETARY=English_United States.1252
> > >>>
> > >>>[4] LC_NUMERIC=C                           LC_TIME=English_United
> > >>>States.1252
> > >>>
> > >>>
> > >>>
> > >>>attached base packages:
> > >>>
> > >>>[1] parallel  stats     graphics  grDevices utils     datasets
>  methods
> > >>>base
> > >>>
> > >>>
> > >>>
> > >>>other attached packages:
> > >>>
> > >>>[1] hugene10sthsentrezgcdf_17.1.0  AnnotationDbi_1.22.6
> > >>>hugene.1.0.st.v1frmavecs_0.0.3 pd.hugene.1.0.st.v1_3.8.0
> > >>>
> > >>>  [5] RSQLite_0.11.4                 DBI_0.2-7
> > >>>frma_1.12.0                    oligo_1.24.2
> > >>>
> > >>>  [9] oligoClasses_1.22.0            affy_1.38.1
> > >>>Biobase_2.20.1                 BiocGenerics_0.6.0
> > >>>
> > >>>
> > >>>
> > >>>loaded via a namespace (and not attached):
> > >>>
> > >>>[1] affxparser_1.32.3     affyio_1.28.0         BiocInstaller_1.10.4
> > >>>Biostrings_2.28.0     bit_1.1-11            codetools_0.2-8
> > >>>
> > >>>  [7] ff_2.2-12             foreach_1.4.1         GenomicRanges_1.12.5
> > >>>IRanges_1.18.4        iterators_1.0.6       MASS_7.3-29
> > >>>
> > >>>[13] preprocessCore_1.22.0 splines_3.0.1         stats4_3.0.1
> > >>>tools_3.0.1           zlibbioc_1.6.0
> > >>
> > >
> >
> > _______________________________________________
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> > Bioconductor@r-project.org
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> > Search the archives:
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> >
>
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